The leukemia-associated ETV6-RUNX1-translocation frequently emerges prenatally. Reverse-transcriptase PCR screening may indicate presence of ETV6-RUNX1 transcripts in random cord blood samples. Subsequent cell enrichment validation finds significantly lower levels than validation applying fluorescence in situ hybridization (FISH) (<10−5 vs. 10−3 to 10−4). Using three FISH probe sets, we screened 179,000 cells from ETV6-RUNX1-positive dilution series, healthy adults and random cord blood samples. The t(12;21) single fusion extra signal translocation probe and the ETV6 break apart probe gave false positive results mimicking ETV6-RUNX1-positive cell levels of 10−3. This questions the paradigm that 1% of newborns have ETV6-RUNX1-positive cells at levels of 10−3 to 10−4. Pediatr Blood Cancer 2014;61:1704–1706. © 2014 Wiley Periodicals, Inc.